I'm unaware that the leaps have any built-in functions for
randomization. But, it should be easy-ish to script. The "rand"
command will generate random numbers (e.g., "rand -N 10" outputs 10
random numbers... see "man rand"). Most programming languages also
have some sort of internal randomization available. You can use those
to add random transformations and/or translations (see manual) to your
leap input files. The thing to make sure of is that each new random
molecule isn't on top of another or in the middle of the protein, etc.
Depending on your needs, you might be able to do something simple-ish
like a a minimum COM distance check to ensure that. You might want to
let leap add the ions and waters after the POPE's so you have less to
worry with in the script.
Of course, there might also be another utility for something like this.
On Sat, May 12, 2012 at 2:09 PM, Massimiliano Porrini <mozz76.gmail.com> wrote:
> Dear all,
>
> I need to randomly place ca. 200 molecules of
> the lipid POPE in my simulation box, and then
> create topology and coordinates files of the
> resulting system:
> protein + counter ions + POPE + water
>
> Is there any t/xleap procedure able to randomly place
> POPE molecules in the box (removing the potential clashing
> water)?
>
> Or I need to use another program?
> If so, can anyone suggest me which is the best solution?
>
> Thanks a lot in advance.
>
> Best,
>
>
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat May 12 2012 - 19:00:03 PDT
